A single polysome-profiling experiment measured 50-nt eGFP-context sequences spanning human transcript UTRs, ClinVar/SNV/indel constructs, engineered target-MRL sequences, and controls. The table retains observed MRLs and author-supplied variant-effect annotations where they can be matched.
Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.
Organism
Human
Taxonomy ID
NCBITaxon:9606
Biosample
CVCL:0063
Reference genome
Not reported / not applicable
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Unmodified uridine (U) IVT mRNA
HEK293T cells were transfected with in-vitro-transcribed reporter mRNA; cells were harvested 12 h later, polysome fractions were collected, fraction-associated sequences were quantified by barcode/NGS, and Mean Ribosome Load (MRL) was computed from relative fraction distributions. The library used a defined 25-nt leader and constant eGFP CDS/3′ context; this is an RNA polysome-profiling MPTA rather than a DNA plasmid MPRA. GEO sample GSM3130443 is the single designed-library run.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (22 of 22)
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Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 22 definitions
element_id
Raw GEO first-column row identifier; it is not guaranteed to be unique in this source file.
utr_sequence
Uppercase tested 50-nt 5′-UTR insert sequence.
utr_length
Length of the tested insert in nucleotides.
uaug_count
Number of ATG motifs in the insert; reading frame is not inferred.
total_reads
GEO total coverage/count field for the construct.
mrl
Published observed mean ribosome load (MRL).
library_subcollection
GEO library label identifying the designed, human UTR, SNV, control, or engineered subcollection.
sequence_status
GEO info4 annotation, such as normal or variant; unannotated when the source is blank or '-'.
variant_type
GEO info3 annotation, such as snv, del, or indel.
variant_id
GEO info1 variant identifier, often an rs identifier.
variant_hgvs
GEO id construct annotation, including the genomic variant description where supplied.
genomic_region
GEO info2 genomic-region annotation.
mother_sequence
GEO mother/reference sequence annotation.
designed_flag
GEO designed boolean flag.
match_score
GEO match score for sequence/design matching.
observed_mrl_diff
Author/repository observed MRL difference between variant and matched normal sequence, from obs_diff.
observed_log2_mrl_diff
Author/repository observed log2 MRL difference, from log_obs_diff.
predicted_log2_mrl_diff
Author/repository predicted log2 MRL difference, from log_pred_diff.
gene_symbol
Gene symbol supplied in the author/repository variant-effect export.
clinical_significance
Clinical-significance annotation supplied in the author/repository variant-effect export.
phenotype
Phenotype annotation supplied in the author/repository variant-effect export.
dbsnp_id
dbSNP identifier supplied in the author/repository variant-effect export.
Quality control
Required a valid A/C/G/T 50-nt sequence, positive finite GEO total, and finite observed MRL. All 100,017 rows passed these filters; no additional effect-size threshold was applied, so normal, variant, synthetic, and control sublibraries are retained. Author-supplied variant-effect fields were joined by the complete construct metadata key.
Curation notes
The first GEO column is a non-unique/shuffled row key in this file; all QC-passing rows are preserved. The effect columns were populated from the authors’ GitHub export snv_phenotype_log_diff.csv using composite construct annotations (sequence, variant metadata, library, and mother sequence), not by assuming the raw first-column key is unique; all 3,002 export rows matched uniquely. Values are supplied author/repository outputs, not recomputed. This mixed library includes human UTRs, SNVs/indels, target-MRL/evolution sequences, and controls, so Variant-focused describes its principal variant-analysis use rather than every subcollection.